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Mutagenesis of p38 MAP Kinase eshtablishes key roles of Phe169 in function and structural dynamics and reveals a novel DFG-out state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYJ PDB ENTRY 1ZYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 10-20% PEG 4000, 0.1 M cacodylic acid, 50 mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.21 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.54 α = 90 b = 70.42 β = 90 c = 75.66 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 4 Mirrors 2004-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.98 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 40 99.6 0.067 25390 25272 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.15 99.9 0.284 0.3 4.9 4.4 4954
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ZYJ 2 24.56 22655 1923 96.95 0.23152 0.22736 0.28045 0.2663 RANDOM 27.472
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.72 -0.05 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.462 r_dihedral_angle_3_deg 19.751 r_dihedral_angle_4_deg 19.395 r_dihedral_angle_1_deg 6.654 r_scangle_it 4.726 r_scbond_it 3.212 r_mcangle_it 2.247 r_angle_refined_deg 2.018 r_mcbond_it 1.299 r_chiral_restr 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.462 r_dihedral_angle_3_deg 19.751 r_dihedral_angle_4_deg 19.395 r_dihedral_angle_1_deg 6.654 r_scangle_it 4.726 r_scbond_it 3.212 r_mcangle_it 2.247 r_angle_refined_deg 2.018 r_mcbond_it 1.299 r_chiral_restr 0.158 r_bond_refined_d 0.023 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2678 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement